The foreign minister of Indonesia, Retno Marsudi, in the country’s capital, Jakarta, on Monday. She handed over an official letter of protest about the confrontation in the South China Sea to the minister counselor of China’s Embassy.CreditDarren Whiteside/Reuters

JAKARTA, Indonesia — China’s Coast Guard rammed one of the country’s fishing boats to pry it free from the Indonesian authorities who had seized it over the weekend, angering the Indonesian government and heightening yet another diplomatic dispute over the South China Sea.

The boat was stopped for fishing illegally in Indonesia’s waters and was being towed to port when the Chinese took it back, leaving its crew in the hands of Indonesia. Jakarta reacted with uncharacteristic fury, summoning the Chinese ambassador to a meeting on Monday.

The high-seas confrontation also indicated that Indonesia might be toughening its stance toward China in the region.

It began at 10 p.m. on Saturday when a special task force vessel operated by the Indonesian Ministry of Maritime Affairs and Fisheries caught a Chinese fishing boat within Indonesia’s maritime 200-mile exclusive economic zone, off the Natuna Islands northwest of Borneo, said Arrmanatha Nasir, a spokesman for Indonesia’s Foreign Ministry.

Indonesian personnel boarded the Chinese boat, the Kway Fey; took its captain and eight-member crew into custody; and began towing the ship back to a base on the Natuna Islands, Mr. Arrmanatha said.

But around midnight, he said, a Chinese Coast Guard vessel, which had been following the Indonesian ship, approached it on or inside the 12-nautical-mile line marking Indonesia’s territorial waters.

The Chinese Coast Guard vessel rammed the fishing boat, apparently to compel the Indonesian authorities to release it, he said.

“To prevent anything else occurring, the Indonesian authorities let go of the Chinese boat and then left toward Natuna, still with eight fishermen and the captain on board,” Mr. Arrmanatha said, adding that the Indonesian crew was “only lightly armed.”

Susi Pudjiastuti, the Maritime affairs and fisheries minister, said Indonesia's efforts to promote peace and regulate fishing in the South China Sea is being usurped.Published OnMarch 21, 2016CreditImage by Beawiharta/Reuters

On Monday morning, Retno Marsudi, the Indonesian foreign minister, met with Sun Weide, minister counselor of China’s Embassy in Jakarta, the capital, and handed over an official letter of protest about the confrontation.

Mr. Sun represented the embassy because the ambassador, Xie Feng, was out of the country.

Later on Monday, a spokeswoman for the Chinese Foreign Ministry, Hua Chunying, called the area where the episode took place “traditional Chinese fishing grounds” and said the coast guard vessel had not entered Indonesian territorial waters.

“China immediately requested Indonesia to release the detained Chinese fishermen and ensure their physical safety,” she said at a regularly scheduled news conference in Beijing.

The confrontation was not the first between Indonesia and China over Chinese fishing vessels near the Natuna Islands, but the government in Jakarta has de-emphasized previous ones or kept them under wraps.

China is one of Indonesia’s largest trading partners and an important market for its commodities, including palm oil and coal. The countries recently signed an agreement for China to build a high-speed rail link between Jakarta and Bandung, the capital of West Java Province.

In March 2013, an Indonesian Maritime Ministry vessel caught a Chinese fishing boat operating in the same region near the Natuna Islands and confiscated the vessel and detained its nine-person crew. Several hours later, the Indonesian ship was confronted by a Chinese vessel, reportedly armed with mounted machine guns and light cannons, which demanded the release of the boat and its crew.

Outgunned and fearing the Chinese ship might open fire, the Indonesian captain complied, and the episode has seldom been spoken of since.

Indonesia’s strong reaction to the latest confrontation, in particular because it may have occurred within its territorial waters, may have been a tipping point in how it deals with Chinese aggressiveness in the South China Sea, said Ian J. Storey, a senior fellow at the Institute of Southeast Asian Studies in Singapore, where he researches South China Sea disputes.

“I think we can say that it is far more serious than the 2013 incident, and I think the Indonesians will be apoplectic,” he said. “Indonesia has tended to downplay them, but they couldn’t this time, and it demonstrates how frustrated that people are getting with China.”

Strain is growing on multiple fronts in the region, where China has territorial disputes with four members of the 10-nation Association of Southeast Asian Nations, known as Asean.

Members of the group have increasingly expressed concern about China’s aggressive posture in the South China Sea, including naval standoffs and land reclamation projects in disputed areas, and the stationing of military personnel and surface-to-air missiles in the Paracel Islands.

Last week, Malaysia’s defense minister, Hishammuddin Hussein, raised the possibility of a “pushback” against China by Southeast Asian nations.

Indonesia is not a claimant in the disputes, but a contentious line drawn by China, which marks its territorial claims to around 90 percent of the maritime region, appears to overlap with part of Indonesia’s maritime 200-mile exclusive economic zone around the Natuna Islands, according to analysts.

Since 1994, Indonesia has sought clarification from China about whether the line encompassed the Natuna Islands or its exclusive economic zone, but, until recently, it had never received an official response from Beijing.

In November, however, China’s Foreign Ministry acknowledged Indonesia’s sovereignty over the Natuna Islands, although it did not address the issue of the exclusive economic zone.

Indonesia has said China’s territorial claims in the South China Sea have no legal basis under international law. That assertion was made most recently by President Joko Widodo during a visit to Japan last March, less than five months after he took office.

One of Mr. Joko’s main foreign policy goals is to transform Indonesia, an archipelagic nation of 250 million people, into a regional maritime power.

The Maritime Ministry has initiated a policy of scuttling all ships confiscated for illegal activities, in particular fishing with Indonesia’s maritime economic zone.

Mr. Arrmanatha said the Chinese Coast Guard might have acted as it did on Saturday because it did not want the Indonesian authorities to confiscate and destroy the vessel.

Indonesia has been building its military presence in the Natuna Islands, according to analysts, and has contemplated deploying eight Apache attack helicopters it bought from the United States.

Patrick Boehler contributed research from Hong Kong.

A version of this article appears in print on , on Page A9 of the New York edition with the headline: Tensions Rise After China’s Coast Guard Frees Fishing Boat Seized by Indonesia. Order Reprints | Today’s Paper | Subscribe